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Showing 42 open source projects for "chem"
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Chem-Parser
Molecule Sketcher and Immediate Parser to Excel, .SMI and 3D SDF
...By enabling rapid structure-to-data mapping, Chem-Parser significantly reduces manual effort in dataset preparation, ensuring consistency and accuracy across large compound libraries. Whether you're building predictive models or managing compound repositories, Chem-Parser offers a user-friendly interface and high-throughput parsing capability that makes it an indispensable addition to any researcher's toolkit. -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
Chem. Inf. Model. 58 (2018), 1343-1355 Check the Wiki for bug reports and fixes. -
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ERmod
Approximate solvation free energy calculator
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER. -
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Aestel
Applications for data management
"Information is data in action", and, consequently, having good quality data is essential. The AESTEL package contains two highly configurable applications for data management: A data loader and a reporting application, i.e. DataLoader and AEREA, respectively. The data loader application applies user-defined instructions to validate, process and load data. The reporting application provides a query builder and spreadsheet template designer. Both applications work with any relational data... -
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...Comput. Aided Mol. Des. 22, 815–829 (2008). 3. Viji, S. N., Prasad, P. A. & Gautham, N. Protein- Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK). J. Chem. Inf. Model. 49, 2687–2694 (2009).
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be downloaded here: https://sourceforge.net/p/genform/code/HEAD/tree/trunk/data/ A first program call could look like this: GenForm ms=SinapinicAcidMs.txt msms=SinapinicAcidMsMs.txt exist out -
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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
...Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole, ...) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities. Code development moved to github: https://github.com/felixplasser/theodore-qc -
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dualword-chem
chemical viewer
chemical viewer written in C++ (Qt, RDKit) Source code: http://github.com/dualword/dualword-chem -
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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The implementation of the methodology presented in the our papers: S. Sibirtsev, C. B. Göbel, A. Jupke, "Automation of a Procedure for the Experimental Investigation of Liquid‐Liquid Phase Separation", Chem. Ing. Tech. 2019, DOI: https://doi.org/10.1002/cite.201900162 This software is available as open software under the 3-Clause BSD license. Simply download the latest ZIP archive. Instructions can be found in the readme files. Check the Wiki for Bug reports and fixes.
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Estimates the maximum random close packing fraction of hard spheres with a distribution of diameters, based upon an algorithm in J. Chem. Phys. 131, 244104 (2009).
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DIFRATE
DIstortion Free Relaxation Analysis TEchnique (DIFRATE) software
...The code is based on the dynamics theory presented in: Albert A. Smith, Matthias Ernst*, Beat Meier*. "Optimized 'detectors' for dynamics analysis in solid-state NMR." J. Chem. Phys, 148, 045104 (2018). DOI: https://doi.org/10.1063/1.5013316 Updates in version 2 allow separation of tumbling in solution and internal motion, include more experiment types, and simplify detector design with singular value decomposition: Albert A. Smith, Matthias Ernst, Beat H. Meier, Fabien Ferrage. "Reducing bias in the analysis of solution-state NMR data with dynamics detectors." (2018) Currently available: http://doi.org/10.1002/anie.201901929 Contact: alsi-nmr@users.sourceforge.net Please contact me if you have any questions. ... -
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This is a standalone program for a) the calculation of diffusion coefficients of sorbates inside nanoporous materials at different loadings by using transition rate constants and for b) solving the master equation for a system consisted of a large number of unit cells per each direction. It is based on the following published paper "Kolokathis, P. D., Braun, O. M.. J. Comput. Chem. 2019, 40, 2053– 2066. DOI: 10.1002/jcc.25857"
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ODFR
Software for simulation of slow motional EPR spectra in aligned media
...The detailed description of all models and approximations used in the program is contained in the following reference: A.Kh.Vorobiev, A.V.Bogdanov, T.S.Yankova, N.A.Chumakova, “Spin probe determination of molecular orientation distribution and rotational mobility in liquid crystals. Model-free approach.”, submitted to Phys. Chem. Chem. Phys., 2018. Please, cite this reference whenever you intend to publish results obtained with the software ODFR. ODFR was created in 2018 in Moscow State University by Prof. Andrey Kh. Vorobiev, mailto: a.kh.vorobiev[[at]]gmail.com -
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Python/xarray tutorial
Python/xarray tutorial for GEOS-Chem users
If the page is loaded successfully, you should see a Jupyter notebook interface. Then, click on the first notebook to get started. Jupyter combines Python code, execution results, plots, custom texts, and even Latex formulas in a single page. Besides using the Jupyter program, you can also view the static notebook on GitHub (e.g the first notebook). Python is free & open-source so can be easily installed on any machines. To best way to get the scientific Python environment is using the Conda... -
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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
...To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at opengrowth-discuss@lists.sourceforge.net. -
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COOP for CRYSTAL
Calculate Crystal Orbital Overlap Population for the CRYSTAL program
...Written by Yang Wang Department of Chemistry,Beijing Normal University Nov. 12th-13th, 2004 Usage: COOP [-v] [-t] [-r] control-file-name -v verbose -t generate control file template -r reserve temporary files A control file is needed to specify the input and output files, type of calculation, indices of basis functions or atoms, energy range, and the maximum number of neighboring cells to be taken into account. An example of the control file can be found in file "coop.con". References: [1] T. Hughbanks and R. Hoffmann, J. Am. Chem. Soc. 105, 3528 (1983). [2] A. Grechnev, R. Ahuja and O. Eriksson, J. Phys.: Condens. Matter 15, 7751 (2003). -
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Med Study Buddy
Physiology questions true-false, med-chem random cards to draw & Czech
Created to help students of medical school to study a large amount of questions. The functionality can be easily extended. -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
...If you use orbkit in your work, please cite it as follows: Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. Comput. Chem. 2016, DOI: 10.1002/jcc.24358. orbkit's documentation can be found at http://orbkit.github.io/ -
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2DMED
Phase Sensitive Detection and Modulated Enhanced Diffraction Software
2DMED it is the second out of two programs which allows implementation of Phase Sensitive Detection (PSD) and/or Modulated Enhanced Diffraction (MED) techniques on the in situ data. This software takes normalized and averaged in situ data in flat file format (FLT) and performs PSD transformation which has been described in Urakawa, A.et al. Chem. Eng. Science 2008, 63, 4902. User can choose demodulation index k and perform several demodulation calculations. This is extremely important since demodulation calculations at k = 2 on in situ powder diffraction data represent implementation of MED method which been described in Chernyshov, D. et al. Acta Cryst. 2011, A67, 327. Demodulated data can be then viewed on 2D and/or 1D plot and analyses with different tools including In Phase Plot, Maximum Amplitude Plot and Positive Pattern Plot. ... -
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ccwatcher
A computational chemistry monitoring, parsing and plotting application
ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies. -
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MSL
http://dx.doi.org/10.1002/jcc.22968
...Reference: Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem. 2012 vol. 33 pages 1645-61 Download article at http://dx.doi.org/10.1002/jcc.22968 -
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Tonto
Tonto - for Quantum Crystallography
...Various linux executables have also been uploaded so you don't need to compile. For non-standard jobs, or for bug-fixes, get the latest version on branches/tonto-3.2 using subversion, like this: svn checkout svn://svn.code.sf.net/p/tonto-chem/code/branches/tonto-3.2 tonto-3.2 DO NOT check out the head, it is too unstable at the moment. -
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Chem Formula Generator
This program generates the chemical formula from the given name.
This program is written in CSharp by B.J Erasmus. It generates the chemical formula from the chemical name that is inputted. Example. Copper(II) Sulfate => CuSO4.
