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Showing 25 open source projects for "chem"
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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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... 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... -
Whether natural disaster, cyberattack, or plain-old human error, data can disappear in the blink of an eye. ConnectWise BCDR (formerly Recover) delivers reliable and secure backup and disaster recovery backed by powerful automation and a 24/7 NOC to get your clients back to work in minutes, not days.
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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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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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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.
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... -
Out-of-the-box scripts. Around-the-clock monitoring. Unmatched automation capabilities. Start doing more with less and exceed service delivery expectations.
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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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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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Comparison of Cartesian Treecodes
Fortran code to compare particle-cluster and cluster-particle treecode
... the targets into an octree and applies a near-field approximation. Particle-cluster is faster when N >> M, and cluster-particle is faster when M >> N. Reference: Boateng, H. A. and Krasny, R., J. Comput. Chem, 34(25), 2013, 2159–2167 This material is based upon work supported by the National Science Foundation under NSF Grants DMS-0854870 and DMS-0915057. Any opinions, findings, and conclusions or recommendations expressed in this material do not necessarily reflect the views of the NSF. -
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OSCAR (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries.
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Collaborative Chemistry Database Tool (CCDBT) is a suit of applications that can perform datafile backup, metadata extraction, database management, metadata visualization and manipulation for cross-group collaboratory in computational chem.
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It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.
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ICE Cafe is Open sourse sequence cromatgram alginer and viewer. The first purpose of this sofware is to find a RNA Editing by Comparing Genomic sequence to RNA sequence, or by using the ICE method developed at Suzuki Lab,Dept Chem&Biotech Tokyo Univ
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Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.
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A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)
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Chemikalienverwaltung (inkl. Bestände) nach deutschem Gesetz. Für Einrichtungen, die laut Einstufung (Schutzstufen) etwas in der Art haben müssen, aber nicht marktwirtschaftlich operieren (Schulen, Bildungsstätten, usw.).
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