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Showing 42 open source projects for "chem"
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Venn is a secure workspace for remote work that isolates and protects work from any personal use on the same computer. Work lives in a secure local enclave that is company controlled, where all data is encrypted and access is managed. Within the enclave – visually indicated by the Blue Border around these applications – business activity is walled off from anything that happens on the personal side. As a result, work and personal uses can now safely coexist on the same computer.
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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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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
...", J. Chem. Theory Comput. 11 (2015), 2517-2524 L.C.Kröger, W.A.Kopp, M.Döntgen, K.Leonhard, "Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations", J. Chem. Theory Comput. 13 (2017), 3955-3960 M.Döntgen, F.Schmalz, W.A.Kopp, L.C.Kröger, K.Leonhard, "Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations", J. 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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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... -
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... of the molecular potential energy surface using mutually orthogonal Latin squares: Application to peptide structures. Biophys. J. 84, 2897 (2003). 2. Arun Prasad, P. & Gautham, N. A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. J. 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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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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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. 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... -
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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 DIFRATE software is used for analysis of NMR relaxation data for dynamics characterization. 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... -
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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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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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ODFR
Software for simulation of slow motional EPR spectra in aligned media
... 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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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. The details can be found in the original publication "OpenGrowth: an automated and rational algorithm for finding new protein ligands" (J. Med. Chem., http://dx.doi.org/10.1021/acs.jmedchem.5b00886). To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top (https://sourceforge.net... -
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COOP for CRYSTAL
Calculate Crystal Orbital Overlap Population for the CRYSTAL program
... -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
... 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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Tonto
Tonto - for Quantum Crystallography
... 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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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... -
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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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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. -
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MSL
http://dx.doi.org/10.1002/jcc.22968
... modeling or design). MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories. 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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piv_clustering
structural clustering of atomic trajectories based on PIV
... is general and the definition of PIV only requires to specify the range of interatomic distances that is relevant for the process under study. Alternatively, also the SPRINT topological coordinates can be employed, that are particularly suited for nanostructures. The output is a partitioning of the trajectory into a few structural clusters (i.e., sets of frames), allowing for simpler analysis and visualization. Please read and cite Gallet & Pietrucci, J. Chem. Phys. 139, 074101 (2013)